Methods for making and using spr microarrays

ABSTRACT

An article, process, and method for surface plasmon resonance plates are described. A substrate is covered with a thin metal film onto which a second thin metal film is deposited. The surface of the second thin metal film is converted to the metal oxide which is used to covalently bond organosilanes to the surface. Reactive organosilanes containing terminal bonding groups are arranged in a plurality of spots that are surrounded by inert organosilanes. Biomolecule attachment to the binding group is detected or measured from surface plasmon signals from the first thin metal film.

BACKGROUND OF THE INVENTION

All patents, patent applications, and publications cited within this application are incorporated herein by reference to the same extent as if each individual patent, patent application or publication was specifically and individually incorporated by reference.

The invention relates generally to surface plasmon resonance substrates and associated methods of analyzing biomolecules. In order to analyze a DNA using surface plasmon resonance (SPR) detection, a metal such as gold having a certain thickness is required on the substrate. For application where DNA is deposited on top of gold there is the problem that gold coated glass slides have not been able to survive DNA printing processes that require corrosive oxidizers, with the gold delaminating from the surface. The gold surface must be modified by using different functionalities, the most popular being thiol chemistry. However, the Au—S bonds are vulnerable to aggressive oxidizers used for some DNA printing process. Thus, there is a need for SPR slides that are able to withstand strong oxidizers used in some DNA printing processes.

SUMMARY OF THE INVENTION

One embodiment is an article comprising: a) a substrate; b) a first metal film overlying the substrate; c) a second thin metal film, the second thin metal film having a first surface facing the first metal film, and a second surface opposed to the first surface; and d) a reactive organosilane covalently bonded to the second surface of the second thin metal film through metal-oxygen-silicon bonds. The second surface opposed to the first surface in the second thin metal film is hereafter referred to as the “upper” surface of the second thin metal film. The first metal film may be gold, silver, or copper and the second thin metal film may be Ti, Zr, Al, Cr, Hf, V, Ta, W, or Pb. Typically, the first metal film can generate surface plasmons and the upper surface of the second thin metal film is used to form chemically stable bonds to the reactive organosilane. As used herein the second thin metal film is sufficiently thin so as to allow extension of an evanescent plasmon wave from said first metal film. The resulting chips can be cleaned with aggressive oxidizers and biomolecules such as DNA, RNA, or proteins can be printed on the reactive organosilane. Chemical interactions with the printed DNA, RNA, or proteins can then be monitored through surface plasmon resonance methods. The second thin metal film may also generate surface plasmons that may interact with the surface plasmons or with surface plasmon effects from the first metal film.

Another embodiment is a process comprising: a) depositing a first metal film on a substrate; b) depositing a second thin metal film on the first metal film; c) converting the upper surface of the second thin metal film to the corresponding metal oxide; and d) reacting a functionalized organosilane with the metal oxide, whereby a reactive organosilane is formed on the upper surface of the second thin metal film. The organosilanes used typically have a reactive silane moiety and an organic substituent (i.e., trichloro-organosilanes). The terms “functionalized” and “inert” when used in connection with “organosilane” refers to the organic substituent of the silane and not the silane moiety. Another embodiment is a process comprising: a) depositing a first metal film on a substrate; b) depositing second thin metal film on the first metal film; c) converting the upper surface of the second thin metal film to the corresponding metal oxide; d) reacting an inert organosilane with the metal oxide; e) patterning the inert organosilane to give a pattern of a plurality of metal oxide spots surrounded by inert organosilane; and f) reacting a functionalized organosilane with the metal oxide, whereby a reactive organosilane is formed in the metal oxide spots on the second thin metal film. Another embodiment is a process comprising: a) depositing a first metal film on a substrate; b) depositing a second thin metal film on the first metal film; c) converting the upper surface of the second thin metal film to the corresponding metal oxide; d) applying a patterned photoresist on the upper surface defining a plurality of spots, the upper surface being exposed between spots; e) reacting an inert organosilane on the metal oxide of the upper surface; f) removing the photoresist to form a plurality of metal oxide spots; and g) reacting a functionalized organosilane with the metal oxide, whereby a reactive organosilane is formed in the metal oxide spots. A similar embodiment is a process comprising: a) depositing a first metal film on a substrate; b) depositing second thin metal film on the first metal film; c) patterning a photoresist on the upper surface into a plurality of spots, the surface of the second thin metal film being exposed between spots; d) converting the surface of the second thin metal film between spots to a metal oxide; e) reacting an inert organosilane with the metal oxide of the second thin metal film; f) removing the photoresist to form a plurality of spots comprising the surface of the second thin metal film; g) converting the surface of the second thin metal film in the spots into a metal oxide, whereby a plurality of metal oxide spots is formed; and h) reacting a functionalized organosilane with the metal oxide spots, whereby a reactive organosilane is formed in the metal oxide spots on the second thin metal film.

Another embodiment is a method, comprising a) providing an article including: i) a substrate; ii) a first metal film overlying the substrate; iii) a second thin metal film overlying the first metal film; iv) an organosilane covalently bonded to the exposed upper surface of the second thin metal film through metal-oxygen-silicon bonds; v) a binding group attached to the organosilane; b) contacting the article with a biomolecule; and c) determining whether or not the biomolecule is bound to the binding group by detecting or measuring a surface plasmon resonance signal generated from the first metal film.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 is a cross-sectional view of a process scheme.

FIG. 2 is a cross-sectional view of a process scheme.

FIG. 3 is a cross sectional view of a process scheme.

FIG. 4 is a cross-sectional view of a process scheme.

DETAILED DESCRIPTION

One embodiment is an article comprising: a) a substrate; b) a first metal film overlying the substrate; c) a second thin metal film overlying the first metal film; and d) a reactive organosilane covalently bonded to the upper surface of the second thin metal film through metal-oxygen-silicon bonds. The first metal film may be gold, silver, or copper and the second thin metal film may be Ti, Zr, Al, Cr, Hf, V, Ta, W, or Pb. Typically, the first metal film can generate surface plasmons and the upper surface of the second metal film is used to form chemically stable bonds to the reactive organosilane. When the second thin metal film is sufficiently thin, the evanescent wave of the surface plasmons generated by the first metal film extend through the second thin metal film and can be used to detect chemical changes near the upper surface of the second thin metal film. Detecting these chemical changes can be used, for example, to monitor biological molecule binding and image dielectric thin films. Typically, the substrate is glass or quartz. In other embodiments, the substrate comprises one face of a prism. The article may further comprise an adhesion metal layer between the substrate and the first metal film. The adhesion metal layer typically is Cr, Ti, W, or any combination thereof.

In many embodiments, the reactive organosilane has a pattern on the surface that is a plurality of spots. In most embodiments, the spots are arranged in a microarray. Hydrophobic material may surround one or more of the reactive organosilane spots. The hydrophobic material may cause a polar liquid (e.g., water) to bead on the reactive organosilane spot, which allows the spot to be used as a microwell. The size of each spot is typically 10-1000 μm in diameter, and the density of spots is typically 100 to 1 million spots per square centimeter. The hydrophobic material typically comprises an inert organosilane covalently bonded to the upper surface of the second thin metal film through metal-oxygen-silicon bonds. The inert organosilane may include, for example, a fluorinated alkyl group. In many embodiments, the reactive organosilane comprises hydroxy groups. The hydroxy groups may be capped with DNA or RNA (e.g., DNA or RNA have been reacted with the hydroxyl groups to form covalent bonds). An example of a reactive organosilane comprises the structure

wherein: R is a reactive group and n=1-20. The reactive group R may comprise, for example, the structures

wherein m=1-10. One example of an inert organosilane comprises the structure

wherein: q=1-4; and p=1-20. In some embodiments, the reactive organosilane comprises the structure

and the hydrophobic material comprises the structure

wherein: R is a reactive group; X is independently at each occurrence a hydrogen or halogen; n=1-20; and q=1-20. The reactive group R may be as described above. The distance between the upper surface of the second thin metal film and the reactive group R on the reactive organosilane, and the distance between the upper surface of the second thin metal film and the non-bonded terminus of the hydrophobic material are controlled through the appropriate selection of alkyl (—(CH₂)_(n)—), or haloalkyl (—(CX₂)_(q)—, where X is a halogen) chain lengths.

Another embodiment is a process comprising: a) depositing a first metal film on a substrate; b) depositing a second thin metal film on the first metal film; c) converting the upper surface of the second thin metal film to the corresponding metal oxide; and d) reacting a functionalized organosilane with the metal oxide, whereby a reactive organosilane is formed on the upper surface of the second thin metal film. The first metal film, the second thin metal film, and the substrate may be as described above. In many embodiments, converting the upper surface of the second thin metal film to the corresponding metal oxide comprises oxygen plasma treatment. In one embodiment, the functionalized organosilane is

wherein: R³ is chlorine or alkoxy; p=1-20; and the reactive organosilane comprises

In other embodiments, the reactive organosilane is

and the process further comprises converting the reactive organosilane to

In some embodiments, the process further comprises patterning the reactive organosilane into a plurality of spots. In one embodiment, the process further comprises reacting the reactive organosilane with DNA or RNA.

Another embodiment is a process comprising: a) depositing a first metal film on a substrate; b) depositing a second thin metal film on the first metal film; c) converting the upper surface of the second thin metal film to the corresponding metal oxide; d) reacting an inert organosilane on the upper surface of the second thin metal film; e) patterning the inert organosilane to give a pattern of a plurality of metal oxide spots surrounded by inert organosilane; and f) reacting a functionalized organosilane with the metal oxide, whereby a reactive organosilane is formed in the metal oxide spots on the second thin metal film. Another embodiment is a process comprising: a) depositing a first metal film on a substrate; b) depositing a second thin metal film on the first metal film; c) converting the upper surface of the second thin metal film to the corresponding metal oxide; d) patterning a photoresist on the upper surface into a plurality of spots, the upper surface being exposed between spots; e) reacting an inert organosilane on the metal oxide of the upper surface; f) removing the photoresist to form a plurality of metal oxide spots; and g) reacting a functionalized organosilane with the metal oxide, whereby a reactive organosilane is formed in the metal oxide spots. A similar embodiment is a process comprising: a) depositing a first metal film on a substrate; b) depositing second thin metal film on the first metal film; c) patterning a photoresist on the upper surface into a plurality of spots, the surface of the second thin metal film being exposed between spots; d) converting the surface of the second thin metal film between spots to a metal oxide; e) reacting an inert organosilane with the metal oxide of the second thin metal film; f) removing the photoresist to form a plurality of spots comprising the surface of the second thin metal film; g) converting the surface of the second thin metal film in the spots into a metal oxide, whereby a plurality of metal oxide spots is formed; and h) reacting a functionalized organosilane with the metal oxide spots, whereby a reactive organosilane is formed in the metal oxide spots on the second thin metal film. The substrate, the first metal film, and the second thin metal film may be as described above. The inert organosilane typically includes a fluorinated alkyl group, for example the structure

wherein: q=1-4; and p=1-20. The functionalized organosilane and the reactive organosilane may be as described above. In one embodiment, the reactive organosilane is

and the process further comprises converting the reactive organosilane to

The size of each spot is typically 10-1000 μm in diameter, and the number the density of spots is typically 100 to 1 million spots per square centimeter. The distance between the upper surface of the second thin metal film and the reactive group R on the reactive organosilane, and the distance between the upper surface of the second thin metal film and the non-bonded terminus of the hydrophobic material are controlled through the appropriate selection of alkyl (—(CH₂)_(n)—), or haloalkyl (—(CX₂)_(q)—, where X is a halogen) chain lengths.

Another embodiment is a method, comprising a) providing an article including: i) a substrate; ii) a first metal film overlying the substrate; iii) a second thin metal film overlying the first metal film; iv) an organosilane covalently bonded to the upper surface of the second thin metal film through metal-oxygen-silicon bonds; and v) a binding group attached to the organosilane; and b) determining whether or not the biomolecule is bound to the binding group by detecting or measuring a surface plasmon resonance signal generated from the first metal film. In some embodiments, the binding group comprises DNA or RNA. The biomolecule is typically DNA, RNA, or a protein. In other embodiments, the binding group is an antigen, an antibody, or a hapten. The organosilane may have a pattern of a plurality of spots. The spots may be arranged in a microarray. The size of each spot is typically 10-1000 μm in diameter, and the number the density of spots is typically 100 to 1 million spots per square centimeter. The first metal film, the second thin metal film, and the glass substrate may be as described above.

EXAMPLES

The following example(s) is illustrative and does not limit the Claims.

A glass substrate was cleaned using Diamaflow 688C. The substrate was soaked in a 1% solution of Diamaflow 688C in DI-water (18MΩ) with and sonicated for 5 minutes. After sonication, the samples were brushed in a fresh solution of Diamaflow and DI-water and sonicated again in DI-water at 30° C. in 15 minutes. The substrate was rinsed for 5 minutes and dried with filtered N₂ gas. Before the metal deposition the substrate was treated with high pressure O₂ plasma for 5 minutes. The plasma cleaning process should happen right before the metal deposition otherwise the surface conditions cannot be precisely controlled. The metal deposition was performed in a Denton Discovery 18 DC magnetron sputtering machine. The base pressure was less than 2×10⁻⁷ Torr. Argon was used as process gas at a pressure of 7.5 mTorr during deposition. The magnetron current was set to 250 mA. First, a 2 nm thick adhesion layer of Cr was deposited followed by deposition of a 47 nm Au layer, followed by deposition of a 10 nm thick layer of Ti.

Deposition of the inert hydrophobic organosilane and reactive organosilane are shown schematically in cross section in FIGS. 1-2. After metal deposition the substrate was photolithographically patterned with photoresist (1) squares (100-200 μm on one side). Following development, an O₂-plasma treatment was used to enhance the bonding of the hydrophobic silane to the Ti. A solution of 1H, 1H, 2H, 2H perfluoroundecyl trichlorosilane was spin deposited, rinsed with toluene, and dried with N₂ gas. The remaining photoresist was removed using a stripper, washed with an isopropyl alcohol and DI-water rinse, and dried with filtered N₂ gas. At this point the Ti surface (2) was exposed as a series of spots surrounded by the hydrophobic silane (3). The exposed Ti surface was treated with O₂ plasma. (Glycidoxypropoxy)trimethoxysilane was spin deposited as described above for the hydrophobic silane to give the reactive organosilane (4) patterned into series of spots, with each spot surrounded by the hydrophobic organosilane (3). The epoxy-reactive silane was converted to a hydroxy-reactive silane by treatment with H₂O/HCl (FIG. 3) or ethylene glycol (FIG. 4). 

1-20. (canceled)
 21. A process, comprising: a) depositing a first metal film on a substrate; b) depositing a second thin metal film on the first metal film; c) converting the upper surface of the second thin metal film to the corresponding metal oxide; and d) reacting a functionalized organosilane with the metal oxide, whereby a reactive organosilane is formed on the upper surface of the second thin metal film.
 22. The process of claim 21, wherein the first metal film is gold, silver, or copper and the second thin metal film is Ti, Zr, Al, Cr, Hf, V, Ta, W, or Pb.
 23. The process of claim 21, wherein the substrate is glass or quartz.
 24. The process of claim 21, wherein converting the upper surface of the second thin metal film to the corresponding metal oxide comprises oxygen plasma treatment.
 25. The process of claim 21, wherein the functionalized organosilane is

wherein: R³ is chlorine or alkoxy; p=1-20; and the reactive organosilane comprises


26. The process of claim 25, wherein the reactive organosilane is

and the process further comprises converting the reactive organosilane to

where m=1-10.
 27. The process of claim 21, further comprising patterning the reactive organosilane into a plurality of spots.
 28. The process of claim 21, wherein the process further comprises reacting the reactive organosilane with DNA or RNA.
 29. A process comprising: a) depositing a first metal film on a substrate; b) depositing a second thin metal film on the first metal film; c) converting the upper surface of the second thin metal film to the corresponding metal oxide; d) reacting an inert organosilane with the metal oxide; e) patterning the inert organosilane to give a pattern of a plurality of metal oxide spots surrounded by inert organosilane; and f) reacting a functionalized organosilane with the metal oxide, whereby a reactive organosilane is formed in the metal oxide spots on the second thin metal film.
 30. The process of claim 29, wherein the inert organosilane includes a fluorinated alkyl group.
 31. The process of claim 30, wherein the inert organosilane comprises

wherein: q=1-4; and p=1-20.
 32. The process of claim 29, wherein the functionalized organosilane is

wherein: R³ is chlorine or alkoxy; p=1-20; and the reactive organosilane comprises


33. The process of claim 32, wherein the reactive organosilane is

and the process further comprises converting the reactive organosilane to

where m=1-10.
 34. The process of claim 29, wherein the size of each spot is 10-1000 μm in diameter.
 35. The process of claim 29, wherein the density of spots is 100 to 1 million per square centimeter.
 36. A method, comprising a) providing an article including: i) a substrate; ii) a first metal film overlying the substrate; iii) a second thin metal film including metal-oxide bonds overlying the first metal film; iv) an organosilane covalently bonded to the exposed upper surface of the second thin metal film through metal-oxygen-silicon bonds; and v) a binding group attached to the organosilane; and b) determining whether or not the biomolecule is bound to the binding group by detecting or measuring a surface plasmon resonance signal generated from the first metal film.
 37. The method of claim 36, wherein the binding group comprises DNA or RNA.
 38. The method of claim 37, wherein the biomolecule is DNA, RNA, or a protein.
 39. The method of claim 36, wherein the binding group is an antigen, an antibody, or a hapten.
 40. The method of claim 36, wherein the organosilane has a pattern of a plurality of spots.
 41. The method of claim 40, wherein the spots are arranged in a microarray.
 42. The method of claim 41, wherein the size of each spot is 10-1000 μm in diameter.
 43. The method of claim 41, wherein the density of spots is 100 to 1 million per square centimeter.
 44. The method of claim 36, wherein the first metal film is gold, silver, or copper and the second thin metal film is Ti, Zr, Al, Cr, Hf, V, Ta, W, or Pb.
 45. The method of claim 36, wherein the substrate is glass or quartz. 